Obvious ones seeing as it's realllyyy far back:
Most early versions did NOT have lab (I remember when that was first added and it was significantly into conquer... at least a year or so)... I know it was pre 2.0 upgrade though so not an issue.
No socketing npc
No bless/enchant npc
No prof lvling npc
No monster hunt npcs
No db leveler
No mall npcs
Rat quest
No composition past +9 (duhh)
Old composition system (double duhhh)
No Dis city or related npcs
No gem composing
No eq quests (again, duhh)
DID have generic basic quests that no one did as well as other main ones. eux for exp, ores and other stuff for an elite coat(?? or maybe bow), met tear, rat fang, refined weps, squama, tg, mine npcs, moon box, sky pass, houses, team/vp, etc
Certain versions DID have magic merchant which would sell rare items for LARGE amounts of gold to regulate economy (usually was like 5x server prices anyways though so it made virtually no diff)
if you want a list of missing systems/features I can remember those a bit better
no exp ball
no pot
no bless
no enchant
no tort/glory/thunder gems
no flowers
no garments
No bottle/gourd/prize
no lock
no item protection
no vip functions
no 120+ items (except weps) 110 was last level of ring fairly sure, boots 120, neck 112 (or 120?? I forget)
No mentor, trade partner, etc
no db leveling
no lotto
no cp
No mall
no ninja
no fan/tower
no horse
I could go on but almost anything I say is painfully obvious. Hopefully there is at least something in there that can be useful though.